Owen Paterson, the Conservative environment secretary, may be blind to the increased risk of flooding across Britain because he is sceptical about climate change science, Labour has said.

Amid warnings of further floods to hit Britain within the next 48 hours, Maria Eagle, the shadow environment secretary, said Paterson had "real questions to answer" about why he was allowing cuts that could affect Britain's ability to deal with severe weather incidents.

She spoke out after Paterson was forced to defend the prospect of 1,200 job losses at the Environment Agency, including reductions in flood risk management.

Eagle told Sky News's Murnaghan programme: "The question is whether Owen Paterson's climate change scepticism – and remember he said that Britain would benefit from climate change – has blinded him to the concerns of increasing risk of flooding, and therefore he hasn't protected budgets."

Britain remains in the grip of the worst run of winter storms for two decades, with 96 flood warnings in place throughout England and Wales and a further 244 areas put on flood alert.

Over the next day or so coastal areas – particularly in southern England – will remain vulnerable due to unusually high tides and the arrival of a strong Atlantic storm.

Eagle said she could not confirm that Labour would increase spending on flood defences, but it would be important to prioritise issues that the government had neglected.

"I'm undertaking that process and we will of course, by the next election, have a manifesto that sets out precisely what our position is," she said. "But the zero-base review is looking line by line at spending and what I've said is that I am not a climate change sceptic – unlike Owen Paterson, I don't think climate change is benefiting Britain."

Paterson, a strong opponent of onshore wind farms, does not deny that climate change is happening but has made several controversial remarks on the subject.

This year he suggested there could be benefits for Britain from climate change, and previously he has said he is sceptical about some of the measures taken to counteract its effects.

"People get very emotional about this subject and I think we should just accept that the climate has been changing for centuries," he said at the Conservative party conference in October. "I think the relief of this latest report is that it shows a really quite modest increase, half of which has already happened. They are talking one to two-and-a-half degrees.

"Remember that for humans, the biggest cause of death is cold in winter, far bigger than heat in summer. It would also lead to longer growing seasons and you could extend growing a little further north into some of the colder areas. I actually see this report as something we need to take seriously but I am rather relieved that it is not as catastrophic in its forecast as we had been led to believe early on and what it is saying is something we can adapt to over time and we are very good as a race at adapting."

Shortly after taking the post of environment secretary in September 2012, he told the Farmers' Guardian: "It is perfectly obvious climate change is there, and there is a human contribution, but I want to be sure the measures we are taking to ameliorate the problem don't create other problems. So that's why I am sceptical."